some changes for ape 3.0-6

[ape.git] / man / read.caic.Rd

diff --git a/man/read.caic.Rd b/man/read.caic.Rd
index 016d8a6cd64c98a241e2880688c2cd3d1084b570..39bc2a1df1a685a30f7d0491927b639955315130 100644 (file)
--- a/man/read.caic.Rd
+++ b/man/read.caic.Rd
@@ -19,12 +19,7 @@ read.caic(file, brlen = NULL, skip = 0, comment.char = "#", ...)
   Read a tree from a file in the format used by the CAIC and MacroCAIc program.
 }
 \value{
-an object of class "phylo" with the following components:
-\item{edge}{a two-column matrix of mode character where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers (these numbers are not treated as numeric, hence the mode character); the nodes are represented with negative numbers (the root being "-1"), and the tips are represented with positive numbers. For each row, the first column gives the ancestor. This representation allows an easy manipulation of the tree, particularly if it is rooted.}
-\item{edge.length}{a numeric vector giving the lengths of the branches given by edge.}
-\item{tip.label}{a vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in edge.}
-\item{node.label}{(optional) a vector of mode character giving the names of the nodes (set to NULL if not available in the file).}
-\item{root.edge}{(optional) a numeric value giving the length of the branch at the root is it exists (NULL otherwise).}
+  an object of class \code{"phylo"}.
 }
 \references{
   Purvis, A. and Rambaut, A. (1995) Comparative analysis by independent